If our qvw file has user restrictions , then if we generated Nprinting PDF based on this, will that PDF automatically comes out with restricted data? or we need to manually input the restrictions to Nprinting as well?

When building nprinting reports you establish a connection to the qvw. I would suggest connecting where you have full access (User name and password -see sample below). In Nprinting, each recipient would then have a filter assigned to them that will send the report to them containing only data that pertains to them. This will mimic the section access functionality into the report